Scorpio Gene-Taxa Benchmark Dataset

Description

Technical info

1. test.fasta :  Contains sequences for model testing.

2. gene_out.fasta: Includes sequences excluded based on gene criteria for model evaluation.

3. taxa_out.fasta :Includes sequences excluded based on taxonomic criteria for model evaluation.

4. val.fasta: Contains sequences for model validation .

5. train.fasta: Contains sequences for model training.

6. metadata.csv: Contains metadata information for sequences in the FASTA files.

7. hierarchical-level.txt : Determines hierarchical levels for triplet training and hierarchical sampling required for Scorpio training.

General Description of FASTA Files:

FASTA files contain sequence data where each sequence entry begins with a header line, starting with ">" followed by a sequence identifier (seqid). 

Retrieving Information from Metadata:

To retrieve metadata information based on the sequence ID (seqid) from the FASTA files:

1. Extract the seqid from the header of the FASTA file
2. Use the extracted seqid to look up the corresponding row in the metadata.csv file.

@article{refahi2024scorpio,
  title={Scorpio: Enhancing Embeddings to Improve Downstream Analysis of DNA sequences},
  author={Refahi, Mohammadsaleh and Sokhansanj, Bahrad A and Mell, Joshua Chang and Brown, James and Yoo, Hyunwoo and Hearne, Gavin and Rosen, Gail},
  journal={bioRxiv},
  pages={2024--07},
  year={2024},
  publisher={Cold Spring Harbor Laboratory}
}